Scientists Receive Grant to Sequence Cowpea Genome

A team of UC Riverside received a nearly $1.6 million grant to sequence the genome of the cowpea.

RIVERSIDE, Calif. (www.ucr.edu) — A team of University of California, Riverside scientists has received a nearly $1.6 million grant from the National Science Foundation to sequence the genome of the cowpea and further their research developing superior cowpea breeding lines.

The cowpea, which also includes black-eyed peas, is one of the most widely grown legume crops in the world and number one source of protein in the human diet in sub-Saharan Africa. It is closely related to soybeans and other warm-season legumes, but is more drought and heat tolerant. It is the most widely grown legume that lacks a published reference genome sequence.

“Despite its relevance to agriculture around the world, cowpea has received relatively little investment for basic research”, said Timothy J. Close, a professor of genetics who is the principal investigator on the grant. “There is a nearly 40-year history of cowpea research here at UC Riverside, dating back to the early years of now-retired Professor Anthony E. Hall with his various other colleagues at UCR and in sub-Saharan Africa. The emphasis has been largely on variety improvement through plant breeding, informed by physiological and genetic research.

“This grant will provide the means to develop some very upstream basic knowledge about the genome of cowpea, and to apply this new knowledge to support the use of theoretically based strategies to combine favorable traits for new variety development. It’s all about making smart choices of parents for crosses, and smart choices in the selection of progeny. In a nutshell, the work can be viewed as the enablement of genome-informed breeding for this important food security crop plant. The starting point in this project is the development of a high-quality reference genome sequence.”

Cowpeas come in many varieties.

A high quality reference genome sequence of the cowpea will put researchers in a better position to develop new cowpea varieties with desirable traits, such as higher yield and quality, disease resistance, pest resistance and drought tolerance that are needed in the face of a growing world population, food security issues and climate change.

With the cowpea genome, the researchers will also be able to do comparative genomic studies with other tropical season legumes, such as soybean (Glycine max) and common bean (Phaseolus vulgaris). The latter species includes kidney beans, navy beans, black beans and pinto beans.

Such comparisons are useful for variety improvement because they reveal shared and unique genome characteristics, which often help to make smart choices of parents and progeny. In addition, basic research itself is accelerated through the reciprocal gain of information as comparisons are made across species.

The warm season legumes, and legumes in general, have a great deal in common biologically, and so they feed off of each other easily through basic research. But, even the favorite model plant of yester year, Arabidopsis thaliana, can be better understood by transferring new knowledge gained from basic research on cowpea and other legumes. This National Science Foundation investment into basic research on cowpea thus not only supports the pipeline of new variety development for small holder farmers, but also elevates knowledge of plants in a much more general sense.

In addition to sequencing the cowpea genome, UC Riverside scientists will conduct further research on the so-called MAGIC (multiparent advanced generation intercross) lines they developed in recent years from eight elite cowpea cultivars. This population will support development of a high-resolution genetic map for use in orientation of DNA sequences along cowpea chromosomes. Superior cowpea breeding lines will be developed by intercrossing MAGIC lines to combine favorable genes from different elite parents.

The National Science Foundation grant is the latest recognition of UC Riverside’s long record of cowpea research.

Since the late 1970s, cowpea research at UCR has contributed to a deeper understanding of the legume’s adaptation to drought, heat and poor soils, and its ability to resist pests and diseases. Collaborative efforts with African cowpea breeders have resulted in development of successful varieties in Senegal, Sudan, Burkina Faso and Ghana, with several new varieties released in the last two years.

UC Riverside is host to a collection of about 6,000 cowpea accessions from around the world. University researchers have released new cowpea varieties in California and West Africa, and have a long-term blackeye pea breeding program funded by the California Dry Bean Advisory Board. The work in West Africa is being done in conjunction with leading breeders in Burkina Faso, Ghana, Mozambique, Nigeria and Senegal, presently supported mainly by the U.S. Government’s Feed the Future Program through two US Agency for International Development (USAID) “Innovation Labs,” with support also coming from the Consultative Group on International Agricultural Research.

UC Riverside researchers conduct cowpea research in the agricultural fields at the UC Riverside campus in Riverside, at the UC Kearney Research and Extension Center in the Central Valley, and also at the Coachella Valley Agricultural Research Station in Thermal, where environmental conditions closely resemble West Africa. Lessons learned breeding in the Coachella Valley have helped boost yield and consumer adoption in Africa.

In total, the UC Riverside cowpea research program has garnered more than $13 million in funding in the last decade, much of it then provided to West African partners as subawards or spent on their behalf for research services, training and travel.

The just-announced National Science Foundation-funded project, known as “BREAD: Advancing the Cowpea Genome for Food Security,” starts April 1, 2016 and will continue for three years.

In addition to Close, five other UC Riverside scientists are involved: Philip A. Roberts, a professor of nematology; Stefano Lonardi, a professor of computer science and engineering; Shizhong Xu, a professor of genetics; and Ph.D. research faculty Bao-Lam Huynh and Maria Munoz-Amatriain who have worked with cowpea in recent years. Close, Roberts and Lonardi are all part of the UC Riverside Institute for Integrative Genome Biology.

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The University of California, Riverside (www.ucr.edu) is a doctoral research university, a living laboratory for groundbreaking exploration of issues critical to Inland Southern California, the state and communities around the world. Reflecting California's diverse culture, UCR's enrollment is now nearly 23,000 students. The campus opened a medical school in 2013 and has reached the heart of the Coachella Valley by way of the UCR Palm Desert Center. The campus has an annual statewide economic impact of more than $1 billion.